MSstatsSampleSize - Githubissues

huang704 commented 5 years ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

Repository: https://github.com/Vitek-Lab/MSstatsSampleSize

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bioc-issue-bot commented 5 years ago

Hi @huang704

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: MSstatsSampleSize
Type: Package
Title: Simulation tool for optimal design of high-dimensional MS-based proteomics experiment
Version: 0.99.0
Date: 2019-10-04
Authors@R: c(
    person("Ting","Huang", , "thuang0703@gmail.com", c("aut", "cre")), 
    person("Meena","Choi", , "mnchoi67@gmail.com", c("aut")),
    person("Olga","Vitek", , "o.vitek@northeastern.edu", role="aut")) 
Description: The packages estimates the variance in the input protein abundance data 
    and simulates data with pre-defined number of biological replicates based on the variance estimation. 
    It reports the mean predictive accuracy of the classifier and mean protein importance over multiple iterations of the simulation. 
Imports: ggplot2, doParallel, caret, gridExtra, reshape2, foreach, parallel, stats, utils, grDevices, graphics,
Suggests: BiocStyle, knitr, rmarkdown, testthat
VignetteBuilder: knitr
biocViews: MassSpectrometry, Proteomics, Software, DifferentialExpression, Classification, PrincipalComponent, 
    ExperimentalDesign, Visualization
License: Artistic-2.0
Depends: R (>= 3.6)
Encoding: UTF-8
LazyData: true
URL: http://msstats.org
BugReports: https://groups.google.com/forum/#!forum/msstats
RoxygenNote: 6.1.1

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bioc-issue-bot commented 5 years ago

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

bioc-issue-bot commented 5 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

d3153f3 Version number bumped

bioc-issue-bot commented 5 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

6b0470b Special characters in manual

bioc-issue-bot commented 5 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

e3b2868 Fix the typos in manual

bioc-issue-bot commented 5 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

bioc-issue-bot commented 5 years ago

Dear Package contributor,

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Congratulations! The package built without errors or warnings on all platforms.

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mtmorgan commented 5 years ago

9 October, 2019

DESCRIPTION

too bad the package does not re-use data structures, even data structures from the same lab group; the software is more fragile and more difficult for interoperability because of that.

vignette

please verify that the code chunks in the vignette output does not spill over the page margins.
MSstatsSampleSize.Rmd:275 model good programming practice by using seq_along() / seq_len() rather than 1:length....
good

R -- comments are on specific lines of code but apply throughout

Methods.R:18 use seq_len() / seq_along() rather than 1:...
Methods.R:19 avoid 'copy-and-append', e.g., y using unlist(lapply()); see http://bioconductor.org/developers/how-to/efficient-code/
designSampleSizeClassification.R:169 message(paste0(...)) can usually be replaced by message(...).
designSampleSizeClassification.R:172 using foreach means that Bioconductor users must learn that package as well; consider using BiocParallel for better interoperability.
there seems to be cut & paste code, one example being simulateDataset.R:131. Consider creating helper functions and using these, so that your code is easier to maintain and more consistent.
simulateDataset.R:182 stop("ERROR: ...") seems redundant, since stop("...") already prints Error: ...").
simulateDataset.R:255 Is stop(message(paste0(...))) intentional, or is stop(...) sufficient?

man

ok

Other

Can the NEWS file be parsed by utils::news()?
nice to see the start on unit tests.

bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

a842762 Revision for bioconductor review

huang704 commented 5 years ago

Thanks for all the comments. The package has been revised according to those comments.

DESCRIPTION

too bad the package does not re-use data structures, even data structures from the same lab group; the software is more fragile and more difficult for interoperability because of that.

Response: We tried to reuse same data structures as other packages from our lab. It is hard to completely re-use the data structures since the input data to these packages are different. But we indeed made one required input of MSstatsSampleSize (annotation data) have same structure and column names as the other packages from our lab.

vignette

please verify that the code chunks in the vignette output does not spill over the page margins.

Response: The vignette has been revised to fit the page width.

MSstatsSampleSize.Rmd:275 model good programming practice by using seq_along() / seq_len() rather than 1:length....

Methods.R:18 use seq_len() / seq_along() rather than 1:...

Response: All the for-loop with 1:length() have been replaced with seq_along() or seq_len().

Methods.R:19 avoid 'copy-and-append', e.g., y using unlist(lapply()); see http://bioconductor.org/developers/how-to/efficient-code/

designSampleSizeClassification.R:169 message(paste0(...)) can usually be replaced by message(...).

designSampleSizeClassification.R:172 using foreach means that Bioconductor users must learn that package as well; consider using BiocParallel for better interoperability.

there seems to be cut & paste code, one example being simulateDataset.R:131. Consider creating helper functions and using these, so that your code is easier to maintain and more consistent.

simulateDataset.R:182 stop("ERROR: ...") seems redundant, since stop("...") already prints Error: ...").

simulateDataset.R:255 Is stop(message(paste0(...))) intentional, or is stop(...) sufficient?

Response: We have used BiocParallel instead of foreach and doParallel for parallel computation. The codes have been revised based on other comments, such as message() or stop().

Can the NEWS file be parsed by utils::news()?

Response: We have made the NEWS file through .Rd file.

bioc-issue-bot commented 5 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, TIMEOUT, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

d86fb45 Compress data

bioc-issue-bot commented 5 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

19c7ecf Fix the R build warning

bioc-issue-bot commented 5 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

bioc-issue-bot commented 5 years ago

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be posed to this issue in the next several days.

Thank you for contributing to Bioconductor!

mtmorgan commented 5 years ago

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/huang704.keys is not empty), then no further steps are required. Otherwise, do the following:

See further instructions at

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for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("MSstatsSampleSize"). The package 'landing page' will be created at

https://bioconductor.org/packages/MSstatsSampleSize

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.

Bioconductor / Contributions

MSstatsSampleSize #1277